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BIOINFORMATICSORIGINAL PAPER

Vol. 26 no. 16 2010, pages 2029–2036

doi:10.1093/bioinformatics/btq331

Systems biology

Deciphering subcellular processes in live imaging datasets via

dynamic probabilistic networks

Kresimir Letinic1,∗,†, Rafael Sebastian2,†, Andrew Barthel3and Derek Toomre4,∗

1Department of Neurobiology and Kavli Institute for Neuroscience, Yale University School of Medicine, 333 Cedar St.,

New Haven, CT 06510, USA,2Department of Computer Sciences, Universitat de Valencia, Av. Vicente Andres

Estelles s/n, 46950 Valencia, Spain,3Department of Biomedical Engineering and4Department of Cell Biology, Yale

University School of Medicine, 333 Cedar St., New Haven, CT, USA 06510

Associate Editor: Alex Bateman

Advance Access publication June 26, 2010

ABSTRACT

Motivation: Designing mathematical tools that can formally describe

the dynamics of complex intracellular processes remains a challenge.

Live cell imaging reveals changes in the cellular states, but current

simple approaches extract only minimal information of a static

snapshot.

Results: We implemented a novel approach for analyzing organelle

behavior in live cell imaging data based on hidden Markov models

(HMMs) and showed that it can determine the number and evolution

of distinct cellular states involved in a biological process. We

analyzed insulin-mediated exocytosis of single Glut4-vesicles, a

process critical for blood glucose homeostasis and impaired in

type II diabetes, by using total internal reflection fluorescence

microscopy (TIRFM). HMM analyses of movie sequences of living

cells reveal that insulin controls spatial and temporal dynamics of

exocytosis via the exocyst, a putative tethering protein complex.

Our studies have validated the proof-of-principle of HMM for cellular

imaging and provided direct evidence for the existence of complex

spatial-temporal regulation of exocytosis in non-polarized cells. We

independently confirmed insulin-dependent spatial regulation by

using static spatial statistics methods.

Conclusion: We propose that HMM-based approach can be

exploited in a wide avenue of cellular processes, especially those

where the changes of cellular states in space and time may be highly

complex and non-obvious, such as in cell polarization, signaling and

developmental processes.

Contact: kresimir.letinic@yale.edu; derek.toomre@yale.edu

Supplementary information: Supplementary data are available at

Bioinformatics online.

Received on January 21, 2010; revised on June 10, 2010; accepted

on June 15, 2010

1

Both fixed and live cell imaging studies often employ only visual

inspection or very limited statistical analysis (such as comparisons

of means) based on the expected effects of some treatment. In static

imaging,avariableofinterestiscomparedunderdifferentconditions

INTRODUCTION

∗To whom correspondence should be addressed.

†The authors wish it to be known that, in their opinion, the first two authors

should be regarded as joint First Authors.

at a single or few time points. Live fluorescence microscopy has

the potential to reveal dynamic changes in a given variable at

multiple time points and under different treatments. The resulting

temporal sequence of data points extracted from a movie sequence

is the starting point for understanding the dynamics of a cellular

process. With the advantages of lower background disturbance and

higher temporal resolution, total internal reflection fluorescence

microscopy (TIRFM) has been widely used for investigating the

dynamics of membrane trafficking events, such as exocytosis of

secretory vesicles (Deng et al., 2009). During exocytosis, a vesicle

generatedinsideacellfuseswiththeplasmamembrane.Thisprocess

is essential for the delivery of membrane receptors and secreted

substances to the cell surface and thus critical for normal cellular

function in all eukaryotic cells.

Live cell imaging generates data sequences of such complexity

that a precise and meaningful description of a biological process

necessitates a dynamic quantitative approach (Patterson et al., 2008;

Phair and Misteli, 2001; Ronneberger et al., 2008; Sebastian et al.,

2006;Talaga,2007;Wangetal.,2006).Characterizationoforganelle

behavior by visual inspection is hampered by the lack of unique

criteria for (and thus user bias in) defining putative ‘functional

cellular states’ and low sampling. It is common to attempt to

formulate these criteria based on measurements of a variable of

interest.To illustrate, in live cell imaging one may wish to determine

how direction and rate of displacement of an organelle changes over

time. A natural approach is to assume that some arbitrary observed

rates or directionalities represent ‘real’ cellular states; e.g. plus-

end motion of a vesicle along a microtubule corresponding to a

kinesin motor and minus-end motion to a dynein. Due to an inherent

variability in noisy biological systems, a manual assignment of two

states will lack flexibility and precision and may fail to characterize

unclearpatterns,e.g.ifanorganellepausesduetocompetingmotors.

Applyingsubjectivecriteriamayalsoresultinoverlookingimportant

aspects of system’s dynamics, which are difficult to observe by

naked eye, precluding complete characterization of the underlying

molecular mechanisms. Robust methods are needed that can deal

with data uncertainty, determine correctly the number of states and

revealthetimingofstatetransitions;suchmethodshavethepotential

to precisely describe spatial and temporal dynamics of biological

processes. In our previous work, we focused on the spatial aspect

of exocytosis (Keller et al., 2001; Letinic et al., 2009; Sebastian

et al., 2006): by using end-point analysis, we were able to obtain a

static description of the distribution of exocytic events on the cell

© The Author 2010. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

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membrane.Typically, we mapped all fusion events that we observed

and then applied tests to determine whether they were distributed

randomly or clustered into hotspots. While such static analyses are

useful, we are often interested in how biological processes evolve

over time as a result of dynamic changes in cellular environment.

The ability to quantitate dynamic changes in cells and subcellular

organelles is extremely important in both basic research and clinical

studies.

In this study, we demonstrate that dynamic probabilistic networks

calledhiddenMarkovModels(HMMs)canuncoverthedynamicsof

cellular states based on the sequence of outcomes of an observable

variable, which conveys information about organelle behavior.

MarkovandhiddenMarkovchainscanbeusedtodescribeprocesses

whose state changes over time in a probabilistic manner (Rabiner,

1989). While in a regular Markov chain model, the states are

directly observable, in a hidden Markov chain model, the only

observable variable is the one that has an outcome influenced by

the hidden states. Since hidden states have a probability distribution

over possible outcomes of the observed variable, the sequence of

observations contains information about the sequence of hidden

states; thus, an algorithm can uncover hidden states. HMMs, first

describedbyBaumandothersinthe1960s(Baumetal.,1970),have

been used in speech recognition, robotics and later in the analysis

of DNA sequence and some single molecule fluorescence studies

(Rabiner, 1989; Talaga, 2007).

From previous biophysical studies we have identified possible

statesofthesystem,thoughtheyarenotdirectlyobservable,theyare

hidden.Twoclueswillhelpusuncoverthesequenceofhiddenstates:

(i) rules that probabilistically link the outcomes of the observable

variable to a particular state; and (ii) rules that probabilistically

relate the states to one another (e.g. State 2 is more likely to

be directly preceded by State 1). These clues are outcome and

transitional probabilities, respectively, the parameters of HMM.

Outcomeprobabilitiesdeterminetheobservableoutcomesgenerated

by hidden states, while transitional probabilities determine state

transitions.

Our approach consists of several steps during which we will:

(i) design ‘observable’ data sequences as the input for HMM;

(ii) estimate multiple model’s parameters (assuming 1–10 states)

via HMM algorithms; (iii) get an indication of the optimal HMM

via model selection methods; and (iv) reveal the trends/patterns

in resulting Markov chain state-paths via statistical tools of

logistic and ordinal logit regression. Expectation–maximization

(EM) algorithms are methods for finding maximum likelihood

estimates that are applicable to many statistical problems, including

hidden Markov chains (Baum et al., 1970; Dellaert, 2002; Dempster

et al., 1977; Rabiner, 1989). EM is a description of a class

of related algorithms, not a specific algorithm; the Baum–Welch

algorithm is an EM algorithm applied to HMMs (Baum et al.,

1970). It can compute maximum likelihood estimates and posterior

mode estimates for the transitional and outcome probabilities of an

HMM, when given only observed sequence of points as training.

A dynamic programming algorithm called the Viterbi algorithm is

used for finding the most likely sequence of hidden states, called

the Viterbi path, given the model parameters uncovered via EM

algorithmandgiventhesequenceofobservedevents(Rabiner,1989;

Viterbi, 1967).

The object of this study is to find dynamic changes in membrane

trafficking events induced by insulin, the hormone critical for

normal glucose metabolism. Glut4 is an insulin-responsive glucose

transporter, expressed in insulin-responsive tissues such as muscle

and fat; Glut4 is responsible for insulin-regulated glucose uptake

into these tissues (Larance et al., 2008; Muretta et al., 2008; Watson

and Pessin, 2007). In the last decade, the insulin-regulated Glut4

translocation to the plasma membrane has been a major focus

in the diabetes field, as dysregulation can cause type II diabetes,

the most common type. While various modes of insulin signaling

have been implicated in Glut4 translocation, traditional assays

were unable to resolve discrete steps in Glut4 vesicle trafficking,

including membrane tethering and fusion steps of vesicles carrying

Glut4. Several studies proposed that an octameric protein complex,

the exocyst, previously suggested to direct secretory vesicles to

specialized sites at the plasma membrane in various cell types

(Matern et al., 2001; Munson and Novick, 2006; Wang and Hsu,

2006), mediates the effect of insulin by tethering Glut4 vesicles

to the plasma membrane (Chen et al., 2007; Inoue et al., 2003).

Resolving how insulin signaling and the exocyst could control the

spatial–temporal dynamics of where and when Glut4 vesicle fuse

is a critical issue in the diabetes field. In this study, we tested

whetherinsulinactingthroughtheexocystcomplexcandynamically

regulate the spatial sites and/or the rate of Glut4 vesicle exocytosis.

Using TIRF microscopy and the HMM mathematical approach, we

provide direct evidence for such regulation. HMM was critical in

that it allowed us to dissect the number of states involved and

real-time kinetics of the exocytic process before and after insulin

stimulation.Specifically,wemodeleddynamicchangesinthespatial

distances and time intervals between consecutive fusion events. For

each imaged cell, we obtained a sequence of spatial distances and

another sequence of time intervals from the sequence of movie

frames. We inputed these observed sequences into an HMM and

obtained two sets of parameters, one for the spatial and other

for the temporal model. Based on these parameters, we extracted

spatial and temporal Markov chain, respectively, that represents the

uncovered sequence of ‘hidden’ states, each of which gives rise to

a unique range of outcomes (i.e. spatial distances or time intervals).

Essentially, by using HMMs, we were able to address precisely the

hiddenstatesthatregulatetraffickinginadipocytesanditsregulation

by insulin.

2METHODS

2.1

3T3-L1 Glut4-GFP cells were cultured, differentiated and stimulated

as previously described. Briefly, 3T3-L1 preadipocytes were grown to

confluence in dulbecco’s modified eagle’s medium (DMEM) containing

10% fetal bovine serum (FBS), L-Glutamine and Pen/Strep (Medium A)

at 37◦C in 5% CO2. Two-day post-confluence (Day 0) differentiation was

induced with methylisobutylxanthine (0.5mM), dexamethasone (0.25µM)

and insulin (1µg/ml). After 3 days, cells were replated on Mattek dishes,

serum starved overnight and switched to an imaging buffer (NaCl, 2.5mM;

KCl,2mM;CaCl2,1.3mM;MgCl2,10mM;HEPES,7.4).WetargetedSec8

usingRNAi;threedifferentsiRNAs(25merdouble-stranded‘stealth’design,

Invitrogen) were first evaluated by double transfecting 293 cells with rat

Sec8-GFP and siRNAs. siRNAs that decreased the newly synthesized Sec8-

GFP (exogenous) were then screened by western blotting for knockdown

of endogenous Sec8 in adipocytes. Quantification showed around 70%

knockdown. For RNAi experiments, cells were transfected twice (3 and

1daysbeforedifferentiation)aspreadipocytes,withSec8orscrambledRNAi

(100nM).

Cell culture and RNAi treatment

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2.2

TIRFM images were acquired using an inverted microscope equipped

with a 1.45 NA 60× TIRFM lens (Olympus, Center Valley, PA), back-

illuminated electron-multiplying charge-coupled device camera (512×512,

16-bit; iXon887; Andor Technologies) and controlled by Andor iQ software

(Andor Technology, South Windsor, CT). Excitation was achieved using a

488nm line of argon laser, under continuous exposure and acquired at 2Hz.

The calculated evanescent field depth was 100 nm. Cells were imaged before

and after insulin stimulation (0.4µM final concentration) at 37◦C for around

15min.TIRFMdatawereuploadedintoacustomizedMatlab-basedsoftware

(Natick, MA) for the detection of exocytic vesicles. All vesicle information

(time, position) was stored and used to generate temporal and spatial maps

of vesicle docking and fusion.

TIRF imaging

2.3

2.3.1 Data sequences

are manually recorded from the image sequences. In our analysis, each

exocytosis event is defined by its location at the plasma membrane and

its occurrence time. If N fusions are observed during the time interval

[0,T], our data are represented by the set X={(xi,yi,ti)}1,...,N. The data

are post-processed to obtain new sequences composed of measured spatial

(Euclidean) distance and time interval (inter-arrival time, t), respectively,

between fusion events. For temporal analysis (first sequence), we measured

inter-arrival times between consecutive fusion events, i.e. Ot=(Xt+1−

Xt)1,...,N−1.Wethenaveragedingroupsof10consecutiveeventstominimize

the impact of outliers, obtaining a new sequence yt=?t

between a designated arbitrary event and 10 events that immediately

preceded it. The resulting sequence contained (N−10) terms for a total of

N events recorded (typically >200–300 events per sequence). Thus, the first

10 events represent a ‘warming interval’ and the observed sequence {y}x

starts with the event 11. Once we obtained the sequence of distances or

inter-arrival times, the range of values was divided into 10 bins, such that

the smallest range of values was in bin 1. In this way, each hidden state can

assign probability to 10 possible outcomes (= bins).

Statistical modeling

For every cell, different exocytosis (events)

k=t−9Ok/10. In the

same way for spatial analysis (second sequence), we averaged the distances

2.3.2 The HMM

(X,Y)=(X0,...,Xn,Y0,...,Yn), where positive real numbers Yi represent

eithertheobservedquantizedvaluesofspatialdistancesorinter-arrivaltimes,

respectively, between fusion events, and the random variables Xiare hidden

cellular states. Y-sequences were generated as described in the previous

section. X-sequence of hidden states was uncovered from the Y-sequence

using HMM algorithms.

The model was parameterized by the parameter space θ =(ξ, A, B); ξ is

the distribution of X0, matrix A is the probability transition matrix of the

hidden chain X (with elements A(k,l)=P{Xi+1=l|Xi=k},k,l∈S, S is the

state space of X); matrix B describes the transitions from Xi to Yi (with

elements B(k,l)=P{Yi=l|Xi=k},k∈S,l∈Q, Q is the state space of Y).

The parameters of the model were determined using an EM algorithm that

iteratively searches for θ that maximizes the likelihood function L(θ)=pθ(y),

i.e. the probability of data as a function of the parameters of the model

{ξ,A,B}. The sequence of hidden states was then reconstructed using the

Viterbi algorithm.

We considered a hidden Markov chain model for

2.3.3 EM algorithm

L(θ). An EM algorithm produces a sequence of θ1,θ2,...,θnthat increase

in likelihood (L(θ0)≤L(θ1)≤...≤L(θn)) (for EM steps, including forward–

backward algorithm, see Rabiner, 1989). The obtained model parameters

represent the expected values of A and B matrix elements conditional on

the data. Starting with θ0, the new parameter was taken to be the θ1and the

procedure was repeated 200 times.The whole cycle was repeated 50 times to

minimize the danger of converging to a local instead of global maximum of

the likelihood function (the confidence intervals for transitional probabilities

wereobtained).Wecalculatedstandarderrorsofthetransitionalprobabilities

The goal of the algorithm is to find θ maximizing

byusingthevaluesoftransitionalprobabilitiesforallthecellsincludedinthe

analysis. Confidence intervals were obtained from standard errors of these

parameters.

We compared HMMs that assume different numbers of states using AIC

(Akaike information criterion). AIC can be seen as the goodness of fit

minus the complexity of the model and it gives a good indication of the

optimal model.AIC measures the fit of an estimated model and is defined as

log(Lk)−|k|, where log(L) is the log-likelihood of the model evaluated at the

MLE (maximum likelihood estimator) and k is the number of the degrees of

freedom. The value of log(L) is given in the output of the HMM, while the

value of k represents the number of free elements in the matrices ξ, A and B.

Clearly, k increases as the number of hidden states increases. We chose the

model with the maximal AIC (see Supplementary Table 1).

2.3.4 TheViterbialgorithm

the most likely sequence of hidden states that generated the observed

outcomes sequence. Multiple sequences of states (paths) can lead to a given

state, but one is the most likely path to that state, called the ‘survivor

path’. This is a fundamental assumption of the algorithm because the

algorithm will examine all possible paths leading to a state and only keep

the one most likely. The best sequence of hidden states maximizes the joint

probability of hidden states and observations, P(X,y)=Pθ(X0=x0,X1=

x1,...,Xn=xn,Y0=y0,Y1=y1,...,Yn=yn). For steps of the algorithm, see

Rabiner (1989).

In the current study, the hidden path represents Markov chain that best

describes the spatial and temporal changes of vesicle fusion events in any

particular cell. In particular, Markov chain includes changes in the cellular

states induced by insulin, specifically at 0.4µM final concentration. The

moment of insulin addition within eachViterbi path is indicated by an arrow.

In the spatial chain, different states give rise to different ranges of distances

between fusion events. In the temporal chain, different states give rise to

different ranges of time intervals between fusion events. Logistic and ordinal

logit regression were used to estimate the odds ratios for Markov chain state

paths (implemented in R).

OnceweselectedthebestHMM,weobtained

2.3.5 Spatial statistical methods

based on spatial statistics methods for use in live cell imaging (Sebastian

et al., 2006). The central concept is distinguishing between a spatial Poisson

process, in which the probability of an event is the same at all locations, and

a clustered process, in which the location of points depends on the location

of nearby points. The relevant statistic is the Ripley K-function, or K(r)

(Diggle, 2003; Ripley, 1981, 1988). We used L(r), because it is a variance-

stabilized version of K(r). To test how far the observed distribution of fusion

events is from Poissonian, we compared the L-plot of an observed process

to the range (envelopes) of L plots of ∼1000 Poisson processes generated

by Monte Carlo simulations using R statistical program. The Monte Carlo

simulation produced a random pattern of fusion event locations across the

cell area using the observed spatial intensity estimate (number of events per

area). The L-function was then calculated for the observed cell and each

simulated Poisson process. The algorithm positions a circle with radius r

on any given event and counts the neighboring events inside the circle; it

repeats this for different radius sizes and then calculates and plots L(r) as

a function of r. The higher the level of clustering, the higher the value of

L(r) will be. L-plots of cells with spatial clustering will be located above the

L-plots of cells with Poissonian distributions of events. A bootstrap method

was used for estimating standard errors and confidence intervals and for the

comparison of different groups.

We previously developed an approach

3

The methodology described has been applied to the study of a

complex problem in live cell imaging, the study of insulin-regulated

exocytosis (Larance et al., 2008; Watson and Pessin, 2007). The

goal was to use our HMM methodology to characterize precisely

RESULTS AND DISCUSSION

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Fig. 1. Imaging of exocytosis in adipocytes. (a) TIRFM image of an

adipocyte (above). An example of a Glut4 vesicle is framed. A sequence

of images shows a fusion event (below). Numbers are shown in seconds.

When a vesicle enters the evanescent field and tethers to the membrane

(asterisk), it increases in fluorescence intensity and appears as a bright spot.

Asitfuses(arrow),thedyeincreasesinintensityandrapidlyspreads,yielding

a characteristic flash. (b)Awestern blot shows an expected decrease of Sec8

byRNAiknockdownonthelevelofendogenousSec8protein(tubulinserves

as a loading control). (c) Spatial maps of fusion events in a control and

a Sec8-depleted (Sec8D) cell. (d) Point processes simulated using Monte

Carlo methods and an example of clusters observed in the control cells after

insulin stimulation (on right). Fusion events appear in different shades of

gray because the time axis (removed because it was not relevant) was color-

coded. The observed clusters resemble simulated spatial clusters. Several

visually apparent clusters are circled.

the spatial temporal dynamics of membrane trafficking events

controlled by insulin. Insulin regulates the number of Glut4 glucose

transporters on the cell surface by stimulating Glut4 vesicles to

exocytoseattheplasmamembrane(Laranceetal.,2008;Watsonand

Pessin, 2007), a process facilitated by the exocyst protein complex

(Chen et al., 2007; Inoue et al., 2003; Matern et al., 2001; Munson

and Novick, 2006; Wang et al., 2006).

Rigorous analysis requires monitoring and analyzing exocytosis

at a single vesicle level. We used an adipocyte cell line that

stably expresses myc-Glut4-GFP and TIRFM to visualize single

vesiclefusion(Fig.1a).Acustom-Matlabprogramwasdevelopedto

facilitate the identification of vesicle fusion at the plasma membrane

by an expert. Spatial–temporal maps of vesicle fusion sites were

recorded for control cells and cells in which we knocked down

a major exocyst subunit, Sec8 (Fig. 1b). The observed data Oi

was a tuple Oi=xi,tiof position and fusion time over the imaged

sequence. Visual inspection of cumulative fusion maps suggested

that the distribution of fusion events changes from relatively

dispersed to more clustered upon insulin stimulation (Fig. 1c).

Nonetheless, these observations did not account for time evolution,

which makes it difficult to assess the sample since the total number

of fusions increases over time.

As a proof-of-principle study of the power and utility of HMM

in live cell imaging of an important topical issue, we applied HMM

to insulin-regulated exocytosis (Larance et al., 2008; Watson and

Pessin, 2007). The goal of the present study was to characterize the

number and evolution of underlying hidden spatial and temporal

states of Glut4 vesicle trafficking events controlled by insulin and

exocyst complex protein, Sec8.

To validate and quantize these changes in real time, we designed

an HMM approach (Fig. 2). In general, our approach consists of the

following steps: (i) calculation of the observed sequence; (ii) EM

algorithm for identifying model parameters, which maximize the

likelihoodoftheobservedsequence;(iii)AIC-basedmodelselection

method to suggest the optimal number of states in the model; and

(iv) the Viterbi algorithm to reveal the most likely sequence of

hidden states.

We first focused on the spatial distribution of Glut4 vesicle

exocytosis and its change upon insulin stimulation. A critical issue

and starting point for this analysis were conceiving an observable

variable that conveys information about the spatial distribution of

vesicle fusion.As more vesicle events occur over time, the distance

between neighboring events decreases. This could significantly

distort the data if we looked at the distance between a new

event and its nearest neighbor. Instead, we considered the distance

between a given event and a small fixed number of preceding

events (Section 2); this metrics does not depend on the overall

density of events. When spatial distribution fluctuates between

less and more clustered, this parameter fluctuates between larger

and smaller values, respectively. We then focused on the rate of

Glut4 vesicle exocytosis and its change upon insulin stimulation.

The parameter of interest was inter-arrival time, or time interval

betweenconsecutiveevents,whichbecomesshorterwhentherateof

exocytosis increases (Section 2). In the case of both spatial distances

and inter-arrival times, we binned the obtained values of parameters

into 10 bins (bin 1=shortest subrange of values; bin 10=longest

subrange of values; this gave 10 possible outcomes of observable

variables distance and time interval). Hidden states will assign

some probability between 0 and 1 to each of these bins/outcomes.

An observed sequence and its associated hidden Markov chain is

shown in Figure 2.

We started our analysis with the spatial data. In many biological

processes, the correct number of hidden states is unknown, even

though one may hypothesize different models based on accumulated

knowledge. We hypothesized that insulin recruits the exocyst at

the cell membrane and thus facilitates tethering of Glut4 vesicles

to specialized hot spots, which are active zones near insulin

receptors. The simplest model would be a two-state model, in

which one state reflects random distribution and another state

reflects more clustered spatial distribution of events (hot spots).

Alternatively, spatial regulation could involve additional molecular

mechanisms and thus more than two states. We ran several models,

assuming 1–10 states (Fig. 3a). For each model (number of states),

we tried dividing the observed values into different number of

bins (2–20bins; Supplementary Table 1). Smaller numbers of bins

resulted in higher AIC values; however, the choice of binning did

not affect the selection of the optimal number of hidden states.

Model selection criterion (AIC) indicated that the two-state model

is the optimal one (Supplementary Tables 1 and 2), regardless of

the number of bins, so we focused specifically on the parameters of

that model (Fig. 3b). We decided to work with 10 bins because 10

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(a)(b)

Fig. 2. A diagram of the approach to model dynamics of exocytosis via HMM. (a) The algorithm: in the first step, a map of fusion events is obtained by

using a custom-made Matlab program. The ‘observed’ sequence of Euclidean distances is derived from the spatial coordinates of mapped fusion events.

This sequence served as input into the EM algorithm, which revealed the most likely model parameters, outcome and transitional probabilities. Finally, the

Viterbi algorithm revealed the most likely sequence of hidden states, based on the model parameters discovered in the previous step. (b) Two-state HMM of

a control adipocytes: HMM output (the hidden chain and probabilities of being in State 1 and 2 at any time point) is superimposed on the observed sequence

of spatial distances. X-axis shows fusion events ordered in temporal sequence. Bins 1–10 (Y-axis on the left side of the graph) represent subranges of the

observed spatial distances between consecutive fusions. There are 10 bins, with bin 1 representing the shortest distances and bin 10 the longest distances. The

posterior probabilities (probability of chain being in State 1 or 2, given the observed sequence) are shown with the corresponding Y-axis on the right side of

the graph that ranges from 0 to 1. Notice that when the probability that the chain is in State 2 equals zero, the probability that the chain is in State 1 equals

one. This makes sense since the chain cannot be in both states simultaneously. In addition, notice that for the most part, the hidden chain is in State 2 when

the probability that the chain is in State 2 is bigger than the probability that the chain is in State 1.

bins provide sufficient detail about the distribution of outcomes of

hidden states. Even though AIC values are the highest when only

two bins are used, two bins results in only two outcomes, which is a

verycruderepresentationoftheobservedvaluesofspatialdistances.

We calculated the following parameters: (i) transitional probabilities

indicatedarelativelysmallprobabilityofswitchingbetweenthetwo

states; (ii) outcome probabilities indicated that ‘State 1’ favors, or

gives more probability to bins with larger spatial distances (we call

it unclustered or ‘UC’ state), while ‘State 2’ favors bins with small

values of distances (we call it clustered or ‘CL’ state, as clusters

become visible after insulin). Thus, at time points when a cell is in

UC state, we will observe longer distances between consecutive

fusion events and when a cell is in CL state, we will observe

shorter distances and clustering of events. We calculated confidence

intervals for the transitional probabilities, especially because of the

small values obtained for the probabilities of switching between the

states and the possibility that the intervals contain zero probability

of switching. Equivalently, we wanted to exclude the possibility that

confidenceintervalsfortheprobabilitiesofstayinginthesamestate,

i.e.notswitching,include1,whichis100%.Themeanprobabilityof

notswitchingfromUCstatewas96.2%(atα=0.001,theconfidence

interval is 94.1–98.4%). The mean probability of not switching

from CL state is 94.2% (at α = 0.001, the confidence interval is

90.8–97.7%). These findings strongly support that the two states of

the Markov chain communicate with each other.

Finally,weobtainedthesequenceofhiddenstatesforthetwo-state

model and compared hidden chains of control and Sec8-depleted

cells.Remarkably,theprobabilitythatthehiddenchainisin‘State2’

dramatically increases, from 5.2% to 72%, after insulin stimulation

(equivalently, the odds of being in State 2 highly significantly

increase, P<0.001; Fig. 3c). This switch occurs rather rapidly,

within a few seconds after the stimulation, and commonly persists

for up to ∼10 min (i.e. until the end of the movie), although in some

cases there is a switch back to ‘State 1’, possibly because the effect

of insulin is transient. Sec8 depletion abolishes this effect, as the

odds that the hidden chain is in ‘State 2’do not change significantly

after insulin stimulation (P=0.8; Fig. 3c). This indicated that Sec8

and thus the exocyst play a role in the spatial regulation of Glut4

exocytosis by insulin and that the effect of insulin is rapid and

transient.

We next analyzed the temporal data. Insulin plays a role in

the release of vesicles from the intracellular pool, allowing them

to travel toward the cell membrane where they fuse. Insulin also

recruits the exocyst at the cell membrane and presumably facilitates

tethering of Glut4 vesicles to the membrane. The simplest model

would be a two-state model, in which one state reflects a slow rate of

events (mostly before insulin) and another state reflects a faster rate

(mostly after insulin). However, a more realistic model would take

into account several levels of regulation. We hypothesized at least

twoinsulin-inducedstates,bothfavoringrelativelyfastrateoffusion

events (fast rate=short intervals). The kinetics of the molecular

switch activated by insulin at the cell membrane (presumably the

exocyst) differs from the kinetics of the switch activated deep

inside the cell (Muretta et al., 2008; Watson and Pessin, 2007). The

complex interplay between these two mechanisms should allow us

to dissect several insulin-induced states. We ran several HMMs,

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Fig. 3. HMM of Glut4-exocytosis: spatial regulation. (a) HMMs assuming 1 (dark green), 2 (blue), 3 (light green), 4 (cyan) or 5 (yellow) states, from a control

cell. Plots of hidden Markov chain state paths corresponding to each model are shown. The x-axis contains both the fusion event number (F # ) and time in

seconds; the vertical arrow shows the time of insulin addition. The individual states of the optimal model (red asterisk), i.e. a two-state model, are labeled on

the right of the plot.Arrowheads mark portions of the state-path when the chain is in State 2, the dominant state after insulin stimulation. (b) Parameters of the

two-state model shown in (a). The two states and their transitional probabilities are shown in the upper right corner. The graph on the left shows probabilities

that the two states assigns to different bins (graph bars and states of the model are color-coded). (c) State-paths of representative control and Sec8-depleted

cells. The vertical arrow shows the moment of insulin addition. The graph on the far right shows the odds ratios, i.e. the factor by which the odds of being in

‘State 2’ change when we add insulin to cells. The odds ratio for control cells is around 46 for control (C) cells and ∼1 for Sec8-depleted (S8) cells.

as before (Fig. 4a and b). Model selection methods indicated that

in control cells, a four-state model was optimal (Supplementary

Table 2) so we focused specifically on the parameters of that

model (Fig. 4c). Transitional probabilities indicated relatively small

probabilities of switching between any pair states, but they were

still higher than those observed in the spatial model. Outcome

probabilities indicated that States 1 and 2 favor larger values of

time intervals, i.e. slower fusion rates (State 1 being the slowest),

while States 3 and 4 favor smaller values of time intervals and thus

faster rates (State 4 being the fastest). Upon insulin stimulation,

the odds of any combination of states favoring shorter intervals

(e.g. State 4) versus the remaining states (States 1–3) are ∼2.4

greater (P<0.001; Fig. 4d). This is in agreement with the notion

that insulin stimulates Glut4 vesicle fusion.As in the case of spatial

regulation, this switch occurs rather rapidly, within a few seconds

after the stimulation, and commonly persists for up to ∼10 min.

Interestingly, Sec8 depletion did not completely abolish the effect

of insulin, as it did in the case of spatial regulation. The effect of

Sec8-depletion was two-prong. First, the optimal model had only

three states: State 2 favored the longest time intervals, i.e. the

slowestrates,State1favoredthemedium-rangeintervalsandState3

favored the shortest intervals and thus the fastest rate (state numbers

are arbitrary). Secondly, the odds of any combination of states

favoring shorter intervals (e.g. States 1 and 3 combined) versus the

remainingstates(State2)wereonly∼1.7greater,suggestingsmaller

impact of insulin than in control cells. The two effects strongly

suggest that the exocyst plays an important role in the regulation

of Glut4 vesicle fusion rate. The loss of one state presumably

corresponds with the loss of one site of insulin action, i.e. at the

cell membrane. In conclusion, HMM was able to dissect various

steps of the temporal process, including the loss of one such step

in treated cells, based on a single observable variable, i.e. the time

interval.

To corroborate our findings obtained using HMM, we used

spatial statistical methods based on L-function (Diggle, 2003;

Ripley, 1988) that we applied to the problem of exocytosis in

previous work (Sebastian et al., 2006). We analyzed cumulative

spatial maps of fusion events obtained by plotting separately all

events before and after insulin stimulation, respectively. In this

case, we disregarded the temporal information and only considered

spatial coordinates of fusion events. Using Monte Carlo methods,

we compared the obtained maps with simulated maps having

completely random distribution of points. We established that the

exocytic spatial point process before insulin stimulation is similar

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Stochastic model of exocytosis

Fig. 4. HMM of Glut4-exocytosis: temporal regulation. (a and b) HMMs assuming 2 (blue), 3 (green), 4 (cyan) or 5 (yellow) states, from a control cell

(a) and a Sec8-depleted cell (b). Plots of state-paths corresponding to various models are shown (axes/labels are as in previous figure). The individual states

of the optimal model (red asterisk) are labeled on the right of the plot (a four-state model for the control cell and a three-state model for the Sec8-depleted

cell). In both cases, arrowheads point to states which favor short intervals between events and which are dominant after insulin. (c and d) Parameters of

the four-state model (c) and the three-state model (d), shown in (a) and (b), respectively. In both cases, Markov model with the states involved and their

transitional probabilities is shown on the right and the graph with the outcome probabilities is on the left (graph bars and model states are color-coded). The

graph on the far right shows the odds ratios, i.e. the factor by which the odds of being in states that favor shorter intervals increase when we add insulin to

cells (see main text).

to random/Poisson process (Fig. 5), in which the probability of

an event is the same at all locations and there is no spatial

dependence among events. However, insulin causes prominent

spatial clustering (L-function plots become significantly different

from random/Poisson; bootstrap P-value=0.01). Sec8-depletion

prevents insulin-induced spatial clustering (most L-plots after

insulin stimulation have a random/Poisson distribution, and are not

significantly different; bootstrap P-value is 0.96) (Fig. 5). Static

end-point analysis of spatial maps thus supports the notion of

spatial clustering induced by insulin. Such regulation of fusion

sites presumably links insulin-receptor signaling at the membrane

to membrane trafficking events. The physiological significance of

spatial regulation remains to be established, but it may promote the

fidelityofinsulinresponsesinceexocystdisturbanceimpairsglucose

uptake.

Since the goal of this work was to validate a new approach based

on HMMs, we chose a system in which we could make expectations

about the behavior of the hidden process (hidden chain), as the

moment of insulin addition served as an external reference point.

We summarize the benefits of using HMMs for analyzing

‘subcellular’ dynamics:

(1) We replace subjective arbitrary criteria with a precise

statistical model for identifying functional cellular states.

(2) Wereplacenoisysequenceofobservations,inwhichitmaybe

hardtodiscernanyobviouspattern,withamodelwithdefined

number of states, thus making rigorous analysis possible.

(3) We can quantitatively interpret real-time dynamics of cellular

processes, while common statistical approaches analyze only

end-points of an experiment.

(4) Wecanlinkdistinctmoleculestodifferentaspectsofthesame

process. For example, we showed that manipulating Sec8

affectsthebehaviorofthespatialandtemporalMarkovchains

in different ways.

(5) We can correlate hidden Markov chains of more than one

process (e.g. in multi-color imaging) and uncover previously

unknown links between various processes.

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K.Letinic et al.

Fig. 5. A comparison of L-curves of control and Sec8-depleted cells.

(a) The scheme illustrates the principle of L-function estimation. The

numbers are counts of events within distance r from an arbitrary event

(marked by the arrow). The number increases as the radius increases. This

counting is repeated for every fusion event. L-function values are estimated

for each radius size. (b) L-curves obtained from the control and Sec8-

depleted cells shown in Figure 1 (plotted as a function of radius r). The

lined area delimits the range of L-function values obtained from a set of

simulated random/Poisson point processes (labeled randomness). There are

two curves for each cell, one obtained before and one obtained after insulin

stimulation. Insulin promotes an upward shift of the L-curve above the

envelopes of randomness only in the control cells (arrow). (c) The range

of L-function values for control and Sec8-depleted cells before and after

insulin stimulation. Notice that ‘before’ and ‘after’ areas do not overlap in

the control, but they mostly overlap in the Sec8-depleted group [the overlaps

arelabeledwithdarkblue(control)anddarkred(sec8-depleted)solidcolors,

respectively].

4

We presented here a methodology based on HMMs and applied it to

the problem of insulin-regulated exocytosis. The method provided

new insight into the spatial and temporal regulation of Glut4 vesicle

exocytosis and exocyst role in determining vesicle fusion sites at

theplasmamembrane.Whiletherainbowoffluorescentproteinshas

revolutionizedtheexplorationofbiology,theextractionandanalysis

of rich live cell datasets remains a new expanding area. Our results

show that HMMs are beneficial in relatively simple cellular systems

and their usefulness in other, more complex processes remains to be

validated. We suggest that HMM can be exploited in a wide avenue

of cellular processes, especially those where the changes of a state in

space, time or both may be ill-defined by conventional criteria, such

as those that occur in cell polarization, signaling and developmental

processes.

CONCLUSIONS

AUTHOR CONTRIBUTIONS

K.L. and D.T. designed research, K.L. and A.B. designed and

implemented the HMM, K.L. and R.S. did statistical data analysis,

K.L. wrote the article with input from A.B. and D.T.

ACKNOWLEDGEMENTS

We thank A. Barron, P. Rakic, T. Koleske and Inhee Chung for

helpful discussions, J. Bogan for suggestions on the paper and

experimental work and for providing the cell line, members of

J. Bogan’s lab for their help with adipocyte protocols, all members

ofD.Toomre’slabforsuggestions,S.CHsuforprovidingantibodies

against exocyst proteins and R.H. Scheller for providing Sec8-

GFP. In addition to the papers in the reference list, the authors

also referred Prof. J. Cheng’s manuscript in preparation, ‘Stochastic

Processes’. K.L. is a predoctoral fellow of the Howard Hughes

Medical Institute.

Funding: National Institute of Health Award (1DP2OD002980-01

and YALE DERC pilot grant to D.T.).

Conflict of Interest: Patents are being filed on these method.

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